# Organization of transcriptional machinery by weak multivalent interactions

> **NIH NIH R01** · UT SOUTHWESTERN MEDICAL CENTER · 2024 · $338,393

## Abstract

Project Summary
Weak multivalent interactions mediated by intrinsically disordered regions (IDRs) of proteins have been proposed
to spatially organize the transcriptional machinery into multi-component clusters, yet we know little about how
these IDRs interact with specific partners to enable functional outcomes. As these interactions are highly
dynamic and cluster-dependent they have been overlooked by conventional strategies to identify protein-protein
interactions. Our preliminary data support our overarching hypothesis that in the context of higher-order clusters
weak multivalent interactions are capable of highly specific hetero-typic interactions leading to functional
organization of the nucleus. Our long-term objective is to understand how weak multivalent interactions organize
specific components of the transcriptional machinery in order to enable gene activation. The objective of this
grant is to investigate the mechanism and function of cluster-mediated interactions of the IDR of MED1, the
largest subunit of the mediator coactivator complex. Mediator is a megadalton complex that bridges DNA-binding
transcription factors with downstream steps of the activation process requiring it to engage dynamically with
many components of the regulatory machinery. While recent structural studies have revealed the architecture of
this complex, the domains responsible for multivalent interactions are dynamic IDRs and remain unresolved. In
particular the MED1 subunit contains a >600 amino acid c-terminal IDR (MED1-IDR) which previously published
studies implicate in cluster formation. Our preliminary data show that MED1-IDR clusters selectively partition
positive regulators of transcription and exclude negative regulators or functionally unrelated yet abundant nuclear
proteins. These data lead us to hypothesize that IDR-mediated selective compartmentalization is a mechanism
to regulate transcription. To test this hypothesis we will confirm and validate the specificity of these cluster-
mediated interactions (Aim 1), characterize the molecular features underlying specificity of these interactions
(Aim 2), and investigate the function of these interactions in various models of gene activation (Aim 3). Upon
completion of these proposed studies, we will understand the role of weak multivalent interactions mediated by
MED1-IDR in organization of specific components of the transcriptional machinery. This contribution is significant
as it will lead to a new appreciation for the function of the prevalent yet often overlooked IDRs in gene activation.
While we focus here on MED1-IDR, the tools and methods developed and the principles learned here can be
applied to other weak multivalent interactions involved in gene regulation or the growing list of biochemical
process regulated by dynamic clustering of regulators.

## Key facts

- **NIH application ID:** 10893453
- **Project number:** 5R01GM147583-03
- **Recipient organization:** UT SOUTHWESTERN MEDICAL CENTER
- **Principal Investigator:** Benjamin Sabari
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $338,393
- **Award type:** 5
- **Project period:** 2022-08-15 → 2027-07-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10893453

## Citation

> US National Institutes of Health, RePORTER application 10893453, Organization of transcriptional machinery by weak multivalent interactions (5R01GM147583-03). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10893453. Licensed CC0.

---

*[NIH grants dataset](/datasets/nih-grants) · CC0 1.0*